Molecular basis of the dual role of the Mlh1-Mlh3 endonuclease in MMR and in meiotic crossover formation

In budding yeast, the MutL homolog heterodimer Mlh1-Mlh3 (MutL gamma) plays a central role in the formation of meiotic crossovers. It is also involved in the repair of a subset of mismatches besides the main mismatch repair (MMR) endonuclease Mlh1-Pms1 (MutL alpha). The heterodimer interface and endonuclease sites of MutL gamma and MutL alpha are located in their C-terminal domain (CTD). The molecular basis of MutL gamma's dual roles in MMR and meiosis is not known. To better understand the specificity of MutL gamma, we characterized the crystal structure of Saccharomyces cerevisiae MutL gamma(CTD). Although MutL gamma(CTD) presents overall similarities with MutL alpha(CTD), it harbors some rearrangement of the surface surrounding the active site, which indicates altered substrate preference. The last amino acids of Mlh1 participate in the Mlh3 endonuclease site as previously reported for Pms1. We characterized mlh1 alleles and showed a critical role of this Mlh1 extreme C terminus both in MMR and in meiotic recombination. We showed that the MutL gamma(CTD) preferentially binds Holliday junctions, contrary to MutL alpha(CTD). We characterized Mlh3 positions on the N-terminal domain (NTD) and CTD that could contribute to the positioning of the NTD close to the CTD in the context of the full-length MutL gamma. Finally, crystal packing revealed an assembly of MutL gamma(CTD) molecules in filament structures. Mutation at the corresponding interfaces reduced crossover formation, suggesting that these superstructures may contribute to the oligomer formation proposed for MutL gamma. This study defines clear divergent features between the MutL homologs and identifies, at the molecular level, their specialization toward MMR or meiotic recombination functions.